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- PDB-5kr2: Protease PR5-SQV -

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Basic information

Entry
Database: PDB / ID: 5kr2
TitleProtease PR5-SQV
ComponentsProtease PR5-SQV
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / E35D / salt-bridge interaction / Natural polymorphism / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Saquinavir / Chem-ROC / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsLiu, Z. / Poole, K.M. / Mahon, B.P. / McKenna, R. / Fanucci, G.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105409 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR031603 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI28571 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution.
Authors: Liu, Z. / Huang, X. / Hu, L. / Pham, L. / Poole, K.M. / Tang, Y. / Mahon, B.P. / Tang, W. / Li, K. / Goldfarb, N.E. / Dunn, B.M. / McKenna, R. / Fanucci, G.E.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease PR5-SQV
B: Protease PR5-SQV
C: Protease PR5-SQV
D: Protease PR5-SQV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0726
Polymers42,7314
Non-polymers1,3422
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-49 kcal/mol
Surface area17810 Å2
2
A: Protease PR5-SQV
B: Protease PR5-SQV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0363
Polymers21,3652
Non-polymers6711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-21 kcal/mol
Surface area9510 Å2
MethodPISA
3
C: Protease PR5-SQV
D: Protease PR5-SQV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0363
Polymers21,3652
Non-polymers6711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-21 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.890, 62.670, 58.400
Angle α, β, γ (deg.)90.00, 98.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protease PR5-SQV


Mass: 10682.636 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: V5YAB1
#2: Chemical ChemComp-ROC / (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide / / Fortovase / SAQUINAVIR / RO 31-8959 / Saquinavir


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 670.841 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H50N6O5 / References: Saquinavir / Comment: medication, antiretroviral*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→26.6 Å / Num. obs: 32248 / % possible obs: 92.6 % / Redundancy: 3.8 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.1.1data reduction
Aimlessdata scaling
PHASER2.1phasing
RefinementResolution: 1.78→22.061 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.99
RfactorNum. reflection% reflection
Rfree0.2326 1999 6.2 %
Rwork0.1903 --
obs0.193 32217 92.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→22.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 98 190 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073192
X-RAY DIFFRACTIONf_angle_d1.0924338
X-RAY DIFFRACTIONf_dihedral_angle_d13.3141184
X-RAY DIFFRACTIONf_chiral_restr0.045516
X-RAY DIFFRACTIONf_plane_restr0.005535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.82450.33161350.24342039X-RAY DIFFRACTION87
1.8245-1.87380.25851370.19582064X-RAY DIFFRACTION90
1.8738-1.92890.25111380.17552089X-RAY DIFFRACTION90
1.9289-1.99110.24011390.182105X-RAY DIFFRACTION90
1.9911-2.06220.24071390.18922103X-RAY DIFFRACTION91
2.0622-2.14470.25971410.182138X-RAY DIFFRACTION91
2.1447-2.24230.21931430.18412150X-RAY DIFFRACTION92
2.2423-2.36040.2611420.19772148X-RAY DIFFRACTION93
2.3604-2.50810.27541440.21152174X-RAY DIFFRACTION93
2.5081-2.70140.24321450.21662184X-RAY DIFFRACTION94
2.7014-2.97270.28541460.21832214X-RAY DIFFRACTION94
2.9727-3.40150.26831480.19552230X-RAY DIFFRACTION95
3.4015-4.28030.16521490.16292261X-RAY DIFFRACTION96
4.2803-22.06240.19361530.17912319X-RAY DIFFRACTION96

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